Articles from the University of Victoria (trainees in italics)
—2024—
115: Morstein J, Bowcut V, Fernando M, Yang Y, Zhu L, Jenkins ML, Evans JT, Guiley KZ, Peacock DM, Krahnke S, Lin Z, Taran KA, Huang BJ, Stephen AG, Burke JE, Lightstone FC, Shokat KM. Targeting Ras-, Rho-, and Rab-family GTPases via a conserved cryptic pocket. Cell. 2024 Sep 6:S0092-8674(24)00908-5. doi: 10.1016/j.cell.2024.08.017.
114: Kotzampasi DM, Papadourakis M, Burke JE, Cournia Z. Free energy landscape of the PI3Kα C-terminal activation. Comput Struct Biotechnol J. 2024 Jul 8;23:3118-3131. doi: 10.1016/j.csbj.2024.07.010. PMID: 39229338; PMCID: PMC11369385.
113: Shaw AL, Suresh S, Parson MAH, Harris NJ, Jenkins ML, Yip CK, Burke JE. Structure of calcineurin bound to PI4KA reveals dual interface in both PI4KA and FAM126A. Structure. 2024 Aug 22:S0969-2126(24)00324-1. doi: 10.1016/j.str.2024.08.007.
112: Bates TA, Trank-Greene M, Nguyenla X, Anastas A, Gurmessa SK, Merutka IR, Dixon SD, Shumate A, Groncki AR, Parson MAH, Ingram JR, Barklis E, Burke JE, Shinde U, Ploegh HL, Tafesse FG. ESAT-6 undergoes self-association at phagosomal pH and an ESAT-6-specific nanobody restricts M. tuberculosis growth in macrophages. Elife. 2024 12:RP91930. doi: 10.7554/eLife.91930. PMID: 38805257; PMCID: PMC11132683.
111: Wan N, Hong Z, Parson MAH, Korfhage JL, Burke JE, Melia TJ, Reinisch KM. Spartin-mediated lipid transfer facilitates lipid droplet turnover. PNAS. 2024
110: Powell CJ, Jenkins ML, Hill TB, Blank ML, Cabo LF, Thompson LR, Burke JE, Boyle JP, Boulanger MJ. Toxoplasma gondii mitochondrial association factor 1b interactome reveals novel binding partners including Ral GTPase accelerating protein α1. JBC. 2024
—2023—
109:Suresh S, Burke JE. Structural basis for the conserved roles of PI4KA and its regulatory partners and their misregulation in disease. Adv in Biol Regulation. 2023
108: Barlow-Busch I, Shaw AL, Burke JE. PI4KA and PIKfyve: Essential phosphoinositide signaling enzymes involved in myriad human diseases. Curr Opin Cell Biol. 2023 83:102207.
107: Harris NJ, Jenkins ML, Nam SE, Rathinaswamy MK, Parson MAH, Ranga-Prasad H, Dalwadi U, Moeller BE, Sheeky E, Hansen SD, Yip CK, Burke JE. Allosteric activation or inhibition of PI3Kγ mediated through conformational changes in the p110γ helical domain. Elife. 2023 12:RP88058.
106: Choi YM, Ajjaji D, Fleming KD, Borbat PP, Jenkins ML, Moeller BE, Fernando S, Bhatia SR, Freed JH, Burke JE, Thiam AR, Airola MV. Structural insights into perilipin 3 membrane association in response to diacylglycerol accumulation. Nat Commun. 2023;14(1):3204.
105. Gehin C, Lone MA, Lee W, Capolupo L, Ho S, Adeyemi AM, Gerkes EH, Stegmann AP, López-Martín E, Bermejo-Sánchez E, Martínez-Delgado B, Zweier C, Kraus C, Popp B, Strehlow V, Gräfe D, Knerr I, Jones ER, Zamuner S, Abriata LA, Kunnathully V, Moeller BE, Vocat A, Rommelaere S, Bocquete JP, Ruchti E, Limoni G, Van Campenhoudt M, Bourgeat S, Henklein P, Gilissen C, van Bon BW, Pfundt R, Willemsen MH, Schieving JH, Leonardi E, Soli F, Murgia A, Guo H, Zhang Q, Xia K, Fagerberg CR, Beier CP, Larsen MJ, Valenzuela I, Fernández-Álvarez P, Xiong S, Śmigiel R, López-González V, Armengol L, Morleo M, Selicorni A, Torella A, Blyth M, Cooper NS, Wilson V, Oegema R, Herenger Y, Garde A, Bruel AL, Tran Mau-Them F, Maddocks AB, Bain JM, Bhat MA, Costain G, Kannu P, Marwaha A, Champaigne NL, Friez MJ, Richardson EB, Gowda VK, Srinivasan VM, Gupta Y, Lim TY, Sanna-Cherchi S, Lemaitre B, Yamaji T, Hanada K, Burke JE, Jakšić AM, McCabe BD, De Los Rios P, Hornemann T, D'Angelo G, Gennarino VA. CERT1 mutations perturb human development by disrupting sphingolipid homeostasis. J Clin Invest. 2023 May 15;133(10):e165019. doi: 10.1172/JCI165019. PMID: 36976648; PMCID: PMC10178846.
104. Burke JE, Triscott J, Emerling BM, Hammond GRV. (2023). Beyond PI3Ks: Targeting phosphoinositide kinases in disease. Nature Reviews Drug Discovery
103.Rathinaswamy MK, Jenkins ML, Duewell BR, Zhang X, Harris NJ, Evans JT, Stariha JTB, Dalwadi U, Fleming KD, Ranga-Prasad H, Yip CK, Williams RL, Hansen SD, Burke JE. (2023). Molecular basis for differential activation of p101 and p84 complexes of PI3Kγ by Ras and GPCRs. Cell Reports.
102.Shaw AL, Parson MAH, Truebestein L, Jenkins ML, Leonard TA, Burke JE.(2023). ATP-competitive and allosteric inhibitors induce differential conformational changes at the autoinhibitory interface of Akt1. Structure.
101.Reinhardt R, Hirzel K, Link G, Eisler SA, Hägele T, Parson MAH, Burke JE, Hausser A, Leonard TA. (2023). PKD autoinhibition in trans regulates activation loop autophosphorylation in cis. Proc Natl Acad Sci U S A.
100. Jenkins ML , Ranga-Prasad H, Parson MAH, Harris NJ , Rathinaswamy MK, Burke JE. (2023). Oncogenic mutations of PIK3CA lead to increased membrane recruitment driven by reorientation of the ABD, p85 and C-terminus. Nature Communications
99. Thibodeau MC, Harris NJ, Jenkins ML, Parson MAH, Evans JT, Scott MK, Shaw AL, Pokorný D, Leonard TA, Burke JE (2023) Molecular basis for the recruitment of the Rab effector protein WDR44 by the GTPase Rab11. Journal of Biological Chemistry
—2022—
98. Matthew AH Parson, Meredith L Jenkins, John E Burke (2022) Investigating how intrinsically disordered regions contribute to protein function using HDX-MS. Biochemical Society Transactions
97. Udit Dalwadi, Elaina Corrado, Kaelin D Fleming, Brandon E Moeller, Sung-Eun Nam, John E Burke, Calvin K Yip (2022) Biochemical Characterization of the TINTIN Module of the NuA4 Complex Reveals Allosteric Regulation of Nucleosome Interaction. Molecular and Cellular Biology
96. John E Burke, Joanna Triscott, Brooke M Emerling, Gerald RV Hammond. (2022) Beyond PI3Ks: targeting phosphoinositide kinases in disease. Nature Reviews Drug Discovery
95. Brendon J Medley, Leif Leclaire, Nicole Thompson, Keira E Mahoney, Benjamin Pluvinage, Matthew AH Parson, John E Burke, Stacy Malaker, Warren Wakarchuk, Alisdair B Boraston (2022) A previously uncharacterized O-glycopeptidase from Akkermansia muciniphila requires the Tn-antigen for cleavage of the peptide bond. Journal of Biological Chemistry
94. Edhriz Siraliev-Perez, Jordan TB Stariha, Reece M Hoffmann, Brenda RS Temple, Qisheng Zhang, Nicole Hajicek, Meredith L Jenkins, John E Burke, John Sondek (2022) Dynamics of allosteric regulation of the phospholipase C-γ isozymes upon recruitment to membranes. Elife.
93. McPhail JA, JE Burke. (2022) Molecular mechanisms of PI4K regulation and their involvement in viral replication. Traffic.
92. Levina A, Fleming KD, Burke JE, Leonard TA. (2022) Activation of the essential kinase PDK1 by phosphoinositide-driven trans-autophosphorylation. Nature Communications. (CRS)
91. Borsari C, Keles E, McPhail JA, Schaefer A, Sriramaratnam R, Goch W, Schaefer T, De Pascale M, Bal W, Gstaiger M, Burke JE, Wymann MP. (2022) Covalent Proximity Scanning of a Distal Cysteine to Target PI3Kα. J Am Chem Soc. (CIHR)
90.Bart Vanhaesebroeck, John E Burke, Ralitsa R Madsen (2022) Precision Targeting of Mutant PI3Kα in Cancer by Selective Degradation. Cancer Discov. (CIHR, CRS)
—2021—
89.Daniel Pokorny, Linda Truebestein, Kaelin D Fleming, John E Burke, Thomas A Leonard (2021) In vitro reconstitution of Sgk3 activation by phosphatidylinositol 3-phosphate. Journal of Biological Chemistry (CRS)
88.Idil Ulengin-Talkish, Matthew AH Parson, Meredith L Jenkins, Jagoree Roy, Alexis ZL Shih, Nicole St-Denis, Gergo Gulyas, Tamas Balla, Anne-Claude Gingras, Péter Várnai, Elizabeth Conibear, John E Burke, Martha S Cyert. (2021) Palmitoylation targets the calcineurin phosphatase to the phosphatidylinositol 4-kinase complex at the plasma membrane. Nature communications (NSERC)
87.Nivea Pereira de Sa, Adam Taouil, Jinwoo Kim, Timothy Clement, Reece M Hoffmann, John E Burke, Robert C Rizzo, Iwao Ojima, Maurizio Del Poeta, Michael V Airola (2021) Structure and inhibition of Cryptococcus neoformans sterylglucosidase to develop antifungal agents. Nature communications (NSERC)
86.Manoj K Rathinaswamy, Udit Dalwadi, Kaelin D Fleming, Carson Adams, Jordan TB Stariha, Els Pardon, Minkyung Baek, Oscar Vadas, Frank DiMaio, Jan Steyaert, Scott D Hansen, Calvin K Yip, John E Burke (2021) Structure of the phosphoinositide 3-kinase (PI3K) p110γ-p101 complex reveals molecular mechanism of GPCR activation. Science Advances (CIHR)
85. Truebestein L, Hornegger H, Anrather D, Hartl M, Fleming KD, Stariha JTB, Pardon E, Steyaert J, Burke JE, Leonard TA (2021) Structure of autoinhibited Akt1 reveals mechanism of PIP3-mediated activation. PNAS (CRS)
84. Gu W, Gao S, Wang H, Fleming KD, Hoffmann RM, Yang JW, Patel NM, Choi YM, Burke JE, Reue J, Airola MV (2021) The middle lipin domain adopts a membrane-binding dimeric protein fold. Nature Communications (NSERC)
83. Rathinaswamy MK*, Fleming KD*, Dalwadi U, Pardon E, Harris NJ, Yip CK, Steyaert J, Burke JE (2021) HDX-MS-optimized approach to characterize nanobodies as tools for biochemical and structural studies of class IB phosphoinositide 3-kinases. Structure
(CIHR)
82. Harris NJ, Jenkins ML, Dalwadi U, Fleming KD, Nam SE, Parson MAH, Yip CK, Burke JE (2021) Biochemical Insight into Novel Rab-GEF Activity of the Mammalian TRAPPIII Complex. Journal of Molecular Biology (NSERC)
81. Baek M, DiMaio F, Anishchenko I, Dauparas J, Ovchinnikov S, Lee GR, Wang J, Cong Q, Kinch LN, Schaeffer RD, Millán C, Park H, Adams C, Glassman CR, DeGiovanni A, Pereira JH, Rodrigues AV, van Dijk AA, Ebrecht AC, Opperman DJ, Sagmeister T, Buhlheller C, Pavkov-Keller T, Rathinaswamy MK, Dalwadi U, Yip CK, Burke JE, Garcia KC, Grishin NV, Adams PD, Read RJ, Baker D (2021) Accurate prediction of protein structures and interactions using a three-track neural network. Science (CIHR)
80. Stariha JTB, Hoffmann RH, Hamelin DJ, Burke, JE* (2021) Probing Protein-Membrane Interactions and Dynamics Using Hydrogen-Deuterium eXchange Mass Spectrometry (HDX-MS) Methods in Molecular Biology. (NSERC)
79. Chen YS, Kozlov G, Armitano J, Moeller BE, Fakih R, Rohaim R, Roux B, Burke JE, Gehring K (2021) Crystal structure of an archaeal CorB magnesium transporter. Nature Communications (NSERC)
78. Rathinaswamy MK, Gaieb Z, Fleming KD, Borsari C, Harris NJ, Moeller BJ, Wymann MP, Amaro RE, Burke JE* (2021) Disease related mutations in PI3Kγ disrupt regulatory C-terminal dynamics and reveals a path to design selective inhibitors. Elife. 10:e64691 (CRS)
—2020—
77. Fienberg S, Eyermann CJ, Arendse LB, Basarab GS, McPhail JA, Burke JE, Chibale K. (2020) Structural Basis for Inhibitor Potency and Selectivity of Plasmodium falciparum Phosphatidylinositol 4-Kinase Inhibitors. ACS Infect Dis. (MMV)
76. Jenkins ML, Harris NJ, Dalwadi U, Fleming KD, Ziemianowicz DS, Rafiei A, Martin EM, Schriemer DC, Yip CK, Burke JE (2020) The substrate specificity of the human TRAPPII complex’s Rab-guanine nucleotide exchange factor activity. Communication Biology. (NSERC)
75. Dobbs JM, Jenkins ML, Burke JE (2020) Escherichia coli and Sf9 Contaminant Databases to Increase Efficiency of Tandem Mass Spectrometry Peptide Identification in Structural Mass Spectrometry Experiments. J Am Soc Mass Spectrom. (NSERC)
74. McPhail JA, Burke JE (2020) Drugging the Phosphoinositide 3-Kinase (PI3K) and Phosphatidylinositol 4-Kinase (PI4K) Family of Enzymes for Treatment of Cancer, Immune Disorders, and Viral/Parasitic Infections. Druggable Lipid Signaling Pathways. Advances in Experimental Medicine and Biology. (NSERC)
73. Seacrist CD, Kuenze G, Hoffmann RM, Moeller BE, Burke JE, Meiler J, Blind RD (2020) Integrated Structural Modeling of Full-Length LRH-1 Reveals Inter-domain Interactions Contribute to Receptor Structure and Function. Structure.(NSERC)
72. Fisher IJ, Jenkins ML, Tall GG, Burke JE, Smrcka, AV (2020) Activation of Phospholipase C β by Gβγ and Gα q Involves C-Terminal Rearrangement to Release Autoinhibition. Structure.(NSERC)
71. Khayyo VI, Hoffmann RM, Wang H, Bell JA, Burke JE, Reue K, Airola MV (2020) Crystal structure of a lipin/Pah phosphatidic acid phosphatase. Nat Commun. (NSERC)
70. Burke JE* (2020) Molecular insight into the auto-inhibition of a master regulator of lipid signalling in human disease. EBio Medicine. (NSERC)
69. Hammond GRV*, Burke JE* (2020) Novel roles of phosphoinositides in signaling, lipid transport, and disease. Current Opinion in Cell Biology. (CIHR, NSERC, CRS)
68. Shin JJH, Liu P, Chan LJ, Ullah A, Pan J, Borchers CH, Burke JE, Stefan C, Smits GJ, Loewen CJR (2020) pH biosensing by PI4P regulates cargo sorting at the TGN. Developmental Cell. (NSERC)
—2019
67. Dornan GD, Stariha JTD, Rathinaswamy MK, Powell CJ, Boulanger MJ, Burke JE* (2019) Defining how oncogenic and developmental mutations of PIK3R1 alter the regulation of class IA phosphoinositide 3-kinases. Structure. (CRS)
66. McPhail JA, Lyoo HR, Pemberton JG, Hoffmann RH, van Elst W, Strating JRPM, Jenkins ML, Stariha JTB, Balla T*, van Kuppeveld FJM*, Burke JE* (2019) Characterization of the Golgi c10orf76-PI4KB complex, and its necessity for Golgi PI4P levels and enterovirus replication. EMBO reports.(CIHR)
65. Rathinaswamy MK, Burke JE. Class I phosphoinositide 3-kinase (PI3K) regulatory subunits and their roles in signaling and disease. (2019). Adv Biol Regul. (CRS)
64. Masson GR*, Burke JE*, Ahn NG, Anand GS, Borchers C, Brier S, Bou-Assaf GM, Engen JR, Englander SW, Faber J, Garlish R, Griffin PR, Gross ML, Guttman M, Hamuro Y, Heck AJR, Houde D, Iacob RE, Jørgensen TJD, Kaltashov IA, Klinman JP, Konermann L, Man P, Mayne L, Pascal BD, Reichmann D, Skehel M, Snijder J, Strutzenberg TS, Underbakke ES, Wagner C, Wales TE, Walters BT, Weis DD, Wilson DJ, Wintrode PL, Zhang Z, Zheng J, Schriemer DC*, Rand KD*. (2019) Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments. Nat Methods. (NSERC)
63. Rageot D, Bohnacker T, Keles E, McPhail JA, Hoffmann RM, Melone A, Borsari C, Sriramaratnam R, Sele AM, Beaufils F, Hebeisen P, Fabbro D, Hillmann P, Burke JE, Wymann MP. (2019) ( S)-4-(Difluoromethyl)-5-(4-(3-methylmorpholino)-6-morpholino-1,3,5-triazin-2-yl)pyridin-2-amine (PQR530), a Potent, Orally Bioavailable, and Brain-Penetrable Dual Inhibitor of Class I PI3K and mTOR Kinase. J Med Chem.(CRS)
62. Shanbhogue P, Hoffmann RM, Airola MV, Maini R, Hamelin DJ, Garcia-Diaz M, Burke JE, Hannun YA. (2019) The juxtamembrane linker in neutral sphingomyelinase-2 functions as an intramolecular allosteric switch that activates the enzyme. .J Biol Chem. (NSERC)
61. Burke JE* (2019) Dynamic structural biology at the protein membrane interface. J Biol Chem. (NSERC, CRS, CIHR)
60. Heitz SD, Hamelin DJ, Hoffmann RM, Greenberg N, Salloum G, Erami Z, Khalil BD, Shymanets A, Steidle EA, Gong GQ, Nürnberg B, Burke JE, Flanagan JU, Bresnick AR, Backer JM. (2019) A Single Discrete Rab5 Binding Site in PI3Kβ is Required for Tumor Cell Invasion. J Biol Chem. (CRS)
—2018—
59. Castro-Falcón G, Seiler GS, Demir Ö, Rathinaswamy MK, Hamelin D, Hoffmann RM, Makowski SL, Letzel AC, Field SJ, Burke JE, Amaro RE, Hughes CC. (2018) Neolymphostin A Is a Covalent Phosphoinositide 3-Kinase (PI3K)/Mammalian Target of Rapamycin (mTOR) Dual Inhibitor That Employs an Unusual Electrophilic Vinylogous Ester. J. Med. Chem (CRS)
58. Vickers C, Liu F, Abe K, Salama-Alber O, Jenkins MJ, Springate CMK, Burke JE, Withers SG, Boraston AB (2018) Endo-fucoidan hydrolases from glycoside hydrolase family 107 (GH107) display structural and mechanistic similarities to α-L-fucosidases from GH29. J Biol Chem. (NSERC)
57. Rageot D, Bohnacker T, Melone A, Langlois JB, Borsari C, Hillmann P, Sele AM, Beaufils F, Zvelebil M, Hebeisen P, Löscher W, Burke JE, Fabbro D, Wymann MP (2018) Discovery and Preclinical Characterization of 5-[4,6-Bis({3-oxa-8-azabicyclo[3.2.1]octan-8-yl})-1,3,5-triazin-2-yl]-4-(difluoromethyl)pyridin-2-amine (PQR620), a Highly Potent and Selective mTORC1/2 Inhibitor for Cancer and Neurological Disorders. J Med Chem.(CRS)
56. Powell CJ, Ramaswam R, Kelsen A, Hamelin DJ, Warshaw DM, Bosch J, Burke JE, Ward, GE, Boulanger MJ (2018) Structural and mechanistic insights into the function of the unconventional class-XIV myosin, MyoA, from Toxoplasma gondii. Proc Natl Acad Sci U S A. (CIHR)
55. Jenkins ML, Margaria JP, Stariha JTB, Hoffmann RM, McPhail JA, Hamelin DJ, Boulanger MJ, Hirsch E, Burke JE. Structural determinants of Rab11 activation by the guanine nucleotide exchange factor SH3BP5. (2018) Nature Communications. (NSERC)
54. Burke JE. Structural Basis for Regulation of Phosphoinositide Kinases and Their Involvement in Human Disease.(2018). Molecular Cell. (CIHR/NSERC/CRS)
53. Brunschwig C, Lawrence N, Taylor D, Abay E, Njoroge M, Basarab GS, Le Manach C, Paquet T, Cabrera DG, Nchinda AT, de Kock C, Wiesner L, Denti P, Waterson D, Blasco B, Leroy D, Witty MJ, Donini C, Duffy J, Wittlin S, White KL, Charman SA, Jiménez-Díaz MB, Angulo-Barturen I, Herreros E, Gamo FJ, Rochford R, Mancama D, Coetzer TL, van der Watt ME, Reader J, Birkholtz LM, Marsh KC, Solapure SM, Burke JE, McPhail JA, Vanaerschot M, Fidock DA, Fish PV, Siegl P, Smith DA, Wirjanata G, Noviyanti R, Price RN, Marfurt J, Silue KD, Street LJ, Chibale K. Antimicrob Agents Chemother. (2018). UCT943, a Next-Generation Plasmodium falciparum PI4K Inhibitor Preclinical Candidate for the Treatment of Malaria. (CIHR)
52. Dornan GL, Dalwadi U, Hamelin DJ, Hoffmann RM, Yip CK, Burke JE. (2018). Probing the Architecture, Dynamics, and Inhibition of the PI4KIIIα/TTC7/FAM126 Complex. J Mol Biol. (CIHR)
51.Lučić I, Rathinaswamy MK, Truebestein L, Hamelin DJ, Burke JE, Leonard TA. (2018). Conformational sampling of membranes by Akt controls its activation and inactivation. Proc Natl Acad Sci U S A. (NSERC)
50. Dornan GL, Burke JE. (2018). Molecular Mechanisms of Human Disease Mediated by Oncogenic and Primary Immunodeficiency Mutations in Class IA Phosphoinositide 3-Kinases. Front Immunol. (NSERC, CRS)
49. Pulkoski-Gross MJ, Jenkins ML, Truman JP, Salama MF, Clarke CJ, Burke JE, Hannun YA, Obeid LM. (2018). An intrinsic lipid-binding interface controls sphingosine kinase 1 function. J Lipid Res.(NSERC)
48. Nnadi CI, Jenkins ML, Gentile DR, Bateman LA, Zaidman D, Balius TE, Nomura DK, Burke JE, Shokat KM, London N. (2018). Novel K-Ras G12C Switch-II Covalent Binders Destabilize Ras and Accelerate Nucleotide Exchange. J Chem Inf Model. (CRS)
—2017—
47. Gentile DR, Rathinaswamy MK, Jenkins ML, Moss SM, Siempelkamp BD, Renslo AR, Burke JE*, Shokat KM*. Ras Binder Induces a Modified Switch-II Pocket in GTP and GDP States. (2017) Cell Chemical Biology (CRS)
46. Powell CJ, Jenkins ML, Parker ML, Ramaswamy R, Kelsen A, Warshaw DM, Ward GE, Burke JE, Boulanger MJ. Dissecting the molecular assembly of the Toxoplasma gondii MyoA motility complex. (2017) Journal of Biological Chemistry (NSERC)
45. Masson GR, Jenkins ML, Burke JE. (2017). An overview of hydrogen deuterium exchange mass spectrometry HDX MS in drug discovery. Expert Opin Drug Discov.
44. McGregor LM, Jenkins ML, Kerwin C, Burke JE, Shokat KM. (2017) Expanding the Scope of Electrophiles Capable of Targeting K-Ras Oncogenes. Biochemistry. (CRS)
43. Siempelkamp BD, Rathinaswamy MK, Jenkins ML, Burke JE. (2017). Molecular mechanism of activation of class IA phosphoinositide 3-kinases (PI3Ks) by membrane-localized HRas. J Biol Chem. (CRS)
42. Takeda AJ, Zhang Y, Dornan GL, Siempelkamp BD, Jenkins ML, Matthews HF, McElwee JJ, Bi W, Seeborg FO, Su HC, Burke JE, Lucas CL. (2017) Novel PIK3CD mutations affecting N-terminal residues of p110δ cause APDS1 in humans. J Allergy Clin Immunol. (NSERC)
41. Bohnacker T, Prota AE, Beaufils F, Burke JE, Melone A, Inglis AJ, Rageot D, Sele AM, Cmiljanovic V, Cmiljanovic N, Bargsten K, Aher A, Akhmanova A, Díaz JF, Fabbro D, Zvelebil M, Williams RL, Steinmetz MO, Wymann MP. (2017). Deconvolution of Buparlisib’s mechanism of action defines specific PI3K and tubulin inhibitors for therapeutic intervention. Nat Commun.
40. Dornan, GD, Siempelkamp, BD, Jenkins, ML, Vadas, O, Lucas, CL, Burke, JE. (2017). Conformational disruption of PI3Kδ regulation by primary immunodeficiency mutations in PIK3CD and PIK3R1. Proc Natl Acad Sci U S A.(NSERC)
39. Noach I, Ficko-Blean E, Pluvinage B, Stuart C, Jenkins ML, Brochu D, Buenbrazo N, Wakarchuk W, Burke JE, Gilbert M, Boraston AB. (2017). Recognition of protein-linked glycans as a determinant of peptidase activity. Proc Natl Acad Sci U S A. (NSERC)
38. McPhail JA, Ottosen EH, Jenkins ML, Burke JE. (2017). The Molecular Basis of Aichi Virus 3A Protein Activation of Phosphatidylinositol 4 Kinase IIIβ, PI4KB, through ACBD3. Structure. (CIHR)
37. Vadas O, Jenkins ML, Dornan GL, Burke JE. (2017) Using Hydrogen–Deuterium Exchange Mass Spectrometry to Examine Protein–Membrane Interactions. Methods in Enzymology. (CIHR)
—2016—
33. KatoN, Comer E, Sakata-Kato T, Sharma A, Sharma M, Maetani M, Bastien J, Brancucci NM, Bittker JA, Corey V, Clarke D, Derbyshire ER, Dornan G, Duffy S, Eckley S, Itoe MA, Koolen KM, Lewis TA, Lui PS, Lukens AK, Lund E, March S, Meibalan E, Meier BC, McPhail J, Mitasev B, Moss EL, Sayes M, VanGessel Y, Wawer MJ, Yoshinaga T, Zeeman AM, Avery VM, Bhatia SN, Burke JE, Catteruccia F, Clardy JC, Clemons PA, Dechering KJ, Duvall JR, Foley MA, Gusovsky F, Kocken CH, Marti M, Morningstar ML, Munoz B, Neafsey DE, Sharma A, Winzeler EA, Wirth DF, Scherer CA, Schreiber SL. (2016). Diversity-oriented synthesis yields novel multistage antimalarial inhibitors. Nature. (CIHR)
32. Haji-Ghassemi O, Gilbert M, Spence J, Schur MJ, Parker MJ, Jenkins ML, Burke JE, van Faassen H, Young NM, Evans SV. (2016). Molecular basis for recognition of the cancer glycobiomarker LacdiNAc (GalNAc(β1-4)GlcNAc) by Wisteria floribunda agglutinin.J Biol Chem. (NSERC)
29. Rutaganira FU, Fowler ML, McPhail JA, Gelman MA, Nguyen K, Xiong A, Dornan GL, Tavshanjian B, Glenn JS, Shokat KM, Burke JE. (2016). Design and Structural Characterization of Potent and Selective Inhibitors of Phosphatidylinositol 4 Kinase IIIβ.J Med Chem. (CIHR)
28. Dornan GL, McPhail JA, Burke JE. (2016). Type III phosphatidylinositol 4 kinases: structure, function, regulation, signalling and involvement in disease. Soc Trans. (CIHR)
27.Fowler ML, McPhail JA, Jenkins ML, Masson GR, Rutaganira FU, Shokat KM, Williams RL, Burke JE. (2016). Using hydrogen deuterium exchange mass spectrometry to engineer optimized constructs for crystallization of protein complexes: Case study of PI4KIIIβ with Rab11. Protein Sci. (NSERC)
—2015—
24. Vadas O., Burke, J.E., (2015) Probing the regulation of membrane signalling complexes and their role in disease using hydrogen deuterium exchange mass spectrometry (HDX-MS). Invited review, Biochem Soc Trans.
23. Burke, J.E., Williams, R.L., (2015). Synergy in activating class I phosphoinositide 3 kinases. Invited featured review, Trends in Biochemical Sciences.
Articles from Postdoc and PhD training (trainees in italics)
—2016—
36. Regulation of a Coupled MARCKS-PI3K Lipid Kinase Circuit by Calmodulin: Single-Molecule Analysis of a Membrane-Bound Signaling Module. Ziemba BP, Swisher GH, Masson G, Burke JE, Williams RL, Falke JJ. Biochemistry. 2016 Nov 22;55(46):6395-6405.
35. Molecular basis of Lys11-polyubiquitin specificity in the deubiquitinase Cezanne. Mevissen TE, Kulathu Y, Mulder MP, Geurink PP, Maslen SL, Gersch M, Elliott PR, Burke JE, van Tol BD, Akutsu M, El Oualid F, Kawasaki M, Freund SM, Ovaa H, Komander D. Nature. 2016 Oct 12;538(7625):402-405.
34. Characterization of Atg38 and NRBF2, a fifth subunit of the autophagic Vps34/PIK3C3 complex. Ohashi Y, Soler N, García Ortegón M, Zhang L, Kirsten ML, Perisic O, Masson GR, Burke JE, Jakobi AJ, Apostolakis AA, Johnson CM, Ohashi M, Ktistakis NT, Sachse C, Williams RL. Autophagy. 2016 Nov;12(11):2129-2144.
31. Regulation of PI3K by PKC and MARCKS: Single-Molecule Analysis of a Reconstituted Signaling Pathway. Ziemba BP, Burke JE, Masson G, Williams RL, Falke JJ. Biophys J. 2016 Apr 26;110(8):1811-25.
30. Methods in the Study of PTEN Structure: X-Ray Crystallography and Hydrogen Deuterium Exchange Mass Spectrometry. Masson GR, Burke JE, Williams RL. Methods Mol Biol. 2016;1388:215-30.
26. The intrinsically disordered tails of PTEN and PTEN-L have distinct roles in regulating substrate specificity and membrane activity. Masson GR, Perisic O, Burke JE, Williams RL. Biochem J. 2016 Jan 15;473(2):135-44.
—2015—
25. Rostislavleva K, Soler N, Ohashi Y, Zhang L, Pardon E, Burke JE, Masson GR, Johnson C, Steyaert J, Ktistakis NT, Williams RL. Structure and flexibility of the endosomal Vps34 complex reveals the basis of its function on membranes. Science. 2015 Oct 9;350(6257):aac7365.
—2014—
22. Clarke, J.H., Giudici, M.L.,Burke, J.E., Williams, R.L., Maloney, D.J., Marugan, J.J., Irvine, R.F, 2014. The function of phosphatidylinositol 5-phosphate 4-kinase γ (PI5P4Kγ) explored using a specific inhibitor that targets the PI5P binding site. Biochemical journal. 466 (2), 359-367.
21. Burke J.E, Inglis, A.J., Perisic, O.,Masson, G.R., Mclaughlin, S., Rutaganira, F., Shokat, K.M., Williams, R.L., 2014. Structures of PI4KIIIß complexes reveal a mechanism for simultaneous recruitment of Rab11 and its effectors. Science. 344(6187), 1035-8.
—2013—
20. Vadas, O., Dbouk, H.A., Shymanets, A., Perisic, O.,Burke J.E., Khali, B.D., Harteneck, C., Nurnberg, B., Backer, J.M., Williams, R.L. (2013) Molecular determinants of PI3Kγ-mediated chemotaxis and transformation downstream of GPCRs. Proceedings of the National Academy of Sciences, 110 (47), 18862-18867.
19. D’Angelo, G., Uemura, T., Chuang, C.C., Polishchuk, E., Santoro, M., Ohvo-Rekila, H., Sato, T., Di Tullio, G., Varriale, A., D’Auria, S., Daniele, T., Capuani, F., Johannes, L., Mattjus, P., Monti, M., Pucci, P., Williams, R.L.,Burke, J.E., Platt, F., Harada, A., De Matteis, M.A. (2013) Vesicular and non-vesicular transport feed distinct glycosylation pathways in the Golgi complex. Nature 01 (7465), 116-120.
18. Burke, J.E., Williams, R.L. (2013) Connecting with an old partner in a new way. Cancer cell, 23 (5), 559-561.
17. Walser, R.,Burke, J.E., Gogvadze, E., Bohnacker, T.,Zhang, X., Hess, D., Küenzi, P., Leitges, M., Hirsch, E., Williams, R.L., Laffargue, M., Wymann, M.P. (2013) PKCβ Phosphorylates PI3Kγ to Activate it and Release it from GPCR Control. PLOS Biology, 11 (6), e1001587.
16. Burke, J.E., Perisic, O., Williams, R.L. Allosteric activation of PI3Kα by oncogenic mutations. (2013) Oncotarget 4 (2) 180-181 Cover article.
15. Cao, J.,Burke, J.E., and Dennis, E.A. Using Hydrogen-Deuterium Exchange Mass Spectrometry to Define the Specific Interactions of the Phospholipase A2 Superfamily with Lipid Substrates, Inhibitors and Membranes. (2013) Journal of Biological Chemistry 288 (3), 1806-1813.
14. Burke, J.E., Williams, R.L. (2013) Dynamic steps in receptor tyrosine kinase mediated activation of class IA phosphoinositide 3-kinases (PI3K) captured by H/D exchange (HDX-MS). Advances in Biological Regulation 53 (1) 97-110.
—2012—
13. Dbouk H.A.,Vadas, O., Shymanets, A.,Burke, J.E., Salamon, R.S., Khalil, B.D., Perisic, O., Shepherd, P.R., Harteneck, C., Harden, T.K., Smrcka, A.V., Taussig, R., Bresnick, A.R., Nürnberg, B., Williams, R.L., and Backer, J.M. (2012) GPCR-mediated activation of p110β via Gβγ is required for cell transformation and chemotaxis. Science signalling 5 (253), ra89 Cover article.
12. Burke, J.E., Perisic, O.,Masson, G.R., Vadas, O., and Williams R.L. (2012) Oncogenic mutations mimic and enhance dynamic events in the natural activation of phosphoinositide 3-kinase p110α (PIK3CA). Proceedings of the National Academy of Sciences 109 (38), 15259-15264.
—2011—
11. Vadas, O.,Burke J.E.,Zhang, X., Berndt, A., and Williams, R.L. (2011) Structural basis for activation and inhibition of class I phosphoinositide 3-kinases. Science signalling 4 (195).
10. Burke, J.E.,Vadas, O., Berndt, A., Finegan, T., Perisic, O., and Williams R.L. (2011) Dynamics of the Phosphoinositide 3-Kinase p110δ Interaction with p85α and Membranes Reveals Aspects of Regulation Distinct from p110α. Structure 19 (8):1127-37.
—2010—
9. Kokotos, G., Hsu, Y.H.,Burke, J.E., Baskakis, C., Kokotos, C.G., Magrioti, V., and Dennis, E.A. (2010) Potent and selective flouroketone inhibitors of group VIA calcium-independent phospholipase A2. Journal of Medicinal Chemistry 53, 3602-3610.
—2009—
8. Hsu, Y. H.,Burke, J.E., Li, S., Woods, V. L., Jr., and Dennis, E. A. (2009) Localizing the membrane binding region of Group VIA Ca2+-independent phospholipase A2 using peptide amide hydrogen/deuterium exchange mass spectrometry. Journal of Biological Chemistry 284, 23652-61.
7. Burke, J.E., Babakhani , A., Gorfe, A.A., Kokotos, G., Li, S., Woods, V.L., Jr., McCammon, J.A., and Dennis, E.A. (2009) Location of inhibitors bound to group IVA phospholipase A2 determined by molecular dynamics and deuterium exchange mass spectrometry. Journal of the American Chemical Society 131, 8083-91.
6. Burke, J.E., Dennis, E.A. (2009) Phospholipase A2Structure/Function and Signaling. Journal of Lipid Research 50, Suppl:S237-42.Most cited paper in Journal of Lipid Research (2008-2013).
5. Burke, J.E., Dennis, E.A. (2009) Phospholipase A2Biochemistry. Cardiovascular drugs and therapy 23, 49-59.
4. Prévost, N., Mitsios, J.V., Kato, H.,Burke, J.E., Dennis, E.A., Shimizu, T., and Shattil, S.J. (2009) Cytosolic Phospholipase A2 α (cPLA2α) and Integrin αIIbβ3 Reinforce Each Other’s Functions During αIIbβ3 Signaling in Platelets. Blood 113, 447-57.
—2008—
3. Burke, J.E., Hsu, Y.H., Deems, R.A., Li, S., Woods, V.L., Jr., and Dennis E.A. (2008) A Phospholipid Substrate Molecule Residing in the Membrane Surface Mediates Opening of the Lid Region in Group IVA Cytosolic Phospholipase A2. Journal of Biological Chemistry 283, 31227-36.
2. Burke, J.E., Karbarz, M.J., Deems, R.A., Li, S., Woods, V.L., Jr., and Dennis, E.A. (2008) Interaction of group IA phospholipase A2 with metal ions and phospholipid vesicles probed with deuterium exchange mass spectrometry, Biochemistry 47, 6451-6459.
1. Hsu, Y. H.,Burke, J.E., Stephens, D.L., Deems, R.A., Li, S., Asmus, K.M., Woods, V.L., Jr., and Dennis, E.A. (2008) Calcium binding rigidifies the C2 domain and the intra-domain interaction of GIVA phospholipase A2 as revealed by hydrogen/deuterium exchange mass spectrometry, Journal of Biological Chemistry 283, 9820-9827.
